In PvP a Jedi Knight would probably win, unless the Smuggler gets the first shot at him. But in a duel that's not possible, and there's no point going into cover (unless you want to get the cover abilities) when your opponent can just run up to you and smash on you; but even if you use your cover abilities there's still the problem of a Jedi Knight smashing your head in on top of you.
Your cover abilities are some of your best, so it'd be kinda silly not to use it until they close in. Between Aim Shot and Sabotage Charge you could probably knock off 1/4 of your opponents HP in about 3 seconds in cover (if not more)... and with proper positioning, use a talented aim shot to throw someone off a ledge... or the stun grenade. Or the nut kick, or...
In the duels I've done as a gunslinger, I've won 'em so far, but it has
been a pretty close fight.